Dr. Ina Huppertz

Research Area: RNA-Binding Proteins in Metabolism and Ageing

Branches: BiochemistryMolecular Biology

Website: Huppertz Lab

1. Research Background

Stem cells, including pluripotent and adult stem cells, possess a unique metabolic landscape that controls their survival and function. The finetuning of redox and metabolic processes is essential for stem cells’ self-renewal, proliferation, and differentiation, which in turn is fundamental to their regenerative capacity. Deviations from this metabolic balance, by contrast, can contribute to ageing and age-associated pathologies, which can particularly impact a person’s quality of life when it is linked to cognitive decline. It is important to continue deepening our understanding of the ageing brain and the potentially rejuvenating neural stem cells (NSCs) that lie dormant or damaged within. The majority of mammalian NSCs (located in the subventricular zone adjacent to the lateral ventricles or the subgranular zone of the hippocampal dentate gyrus) remain in a quiescent state and undergo self-renewal via a slow cell cycle. However, certain stimuli activate these quiescent NSCs causing them to proliferate at a much higher rate. This population of more rapidly proliferating NSCs, termed neural progenitor cells (NPCs), can in turn differentiate into neurons, astrocytes, or oligodendrocytes depending on the received cue. Metabolite utilization via primary metabolic pathways is a key regulator in the context of NSCs’ survival and regenerative function. While quiescent NSCs are thought to preferentially utilize glycolysis or fatty acid oxidation to meet the low metabolic requirements of dormancy, activation and differentiation towards a neuronal lineage is associated with an increased reliance on oxidative phosphorylation. However, ageing impairs mitochondrial respiration by damaging the machinery necessary for controlled activation of the NSCs’ proliferation and thereby directly impacts adult neurogenesis.

2. Research questions addressed by the group:

While transcriptional changes have received scholarly attention for many decades, RNA-binding proteins (RBPs) have only recently taken centre stage as regulators of metabolism. RBPs are a versatile group of proteins that can facilitate short- and long-term metabolic adjustments of cells undergoing cell division and differentiation. Furthermore, RBPs can integrate metabolic stimuli through, for example, post-translational modifications, changes in localization or metabolite availability. One example of a canonical RBP that impacts the metabolic setup of the cell is YBX3. By binding to the 3’ untranslated region, YBX3 stabilizes the transcript of the amino acid transporter SLC7A5, and thereby indirectly alters the availability of large, neutral amino acids in the cell. In addition, many essential metabolic enzymes have been identified to bind RNA in different cell types and organisms. Two simplistic modes of RNA–enzyme interactions can be envisioned. On the one hand, metabolic enzymes might moonlight as RBPs and regulate the fate of their target RNAs. On the other hand, RNA might regulate these enzymes, a process we have recently described for the glycolytic enzyme Enolase 1. This very large class of non-canonical RBPs might form a novel layer of metabolic regulation.

Our overarching aim is to utilize the metabolically dynamic system of pluripotent and differentiating stem cells during ageing to elucidate the following questions and discover the involvement of canonical and non-canonical RBPs therein:

  1. What regulates the metabolic alterations that ageing NSCs undergo?
  2. What role does metabolism play in the ageing process of NSCs?
  3. What coordinates cytosolic and mitochondrial metabolic pathways in ageing NSCs?

You will have the possibility to openly discuss the direction of your future PhD project and join a young and dynamic team of researchers. Your project will be at the interface of RNA biology, metabolism and stem cell research in the context of ageing and will be supported by all team members. Furthermore, we are coordinating the Rhineland RNA club to further expand our network of collaborators, which will provide a platform for regular presentations to a wider audience.

3. Applied Methods and model organisms:

Our lab strives to find the best tools and methods to answer our questions. This involves the usage of well-established molecular biology-based and biochemical assays to high-throughput screens. It also requires the development of novel techniques to ensure that our research is at the cutting edge and pushes the boundaries of what is currently possible. Applied methods include:

  • Biochemical, molecular and cellular biology-based methods, such as molecular cloning, Western blotting, immunofluorescence, etc.
  • Cutting-edge RNA-related techniques, such as qPCR, crosslinking and immunoprecipitation (CLIP), RNA-interactome capture, RNA sequencing (including single-cell RNAseq).
  • CRISPR/Cas9-mediated genome editing and CRISPR screens
  • Fluorescence activated cell sorting (FACS)
  • Proteomics and metabolomics

Our current model systems are mammalian cell cultures including mouse embryonic stem cells and human induced pluripotent stem cells. Long-term we are interested in expanding our portfolio to include organoids.

4. Desirable skills and qualifications:

We seek an enthusiastic, driven and creative PhD student who has a strong interest in RNA biology and metabolism. Skills in all of the above-mentioned techniques can be acquired as part of your PhD. However, prior knowledge in any of them will be advantageous. Our group that has been established in August 2022 is looking for new members, who want to become an integral part in shaping the future of our research group in an open exchange with your colleagues and supervisor. Your excitement excites us!

5. References and key publications:

  • Huppertz, I., Perez-Perri, J.I., Mantas, P., Sekaran, T., Schwarzl, T., Russo, F., Ferring-Appel, D., Koskova, Z., Dimitrova-Paternoga, L., Kafkia, E., Hennig, J., Neveu, P.A., Patil, K., Hentze, M.W. Riboregulation of enolase 1 activity controls glycolysis and embryonic stem cell differentiation. Mol Cell. 22, S1097-27650 (2022).
  • Hallegger, M.*, Chakrabarti, A.M.*, Lee, F.C.Y.*, Lee, B.L., Amalietti A., Odeh, H.M., Copley, K.E., Rubien, J.D., Portz, B., Kuret, K., Huppertz, I., Rau, F., Patani, R., Fawzi N.L., Shorter, J., Luscombe, N.M., Ule, J. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell 184,1–17 (2021).
  • Cooke, A., Schwarzl, T. *, Huppertz, I. *,Y, Kramer, G., Mantas, P., Alleaume, A.M., Huber, W., Krijgsveld, J., Hentze, M.W.Y The RNA-binding protein YBX3 controls amino acid levels by regulating SLC mRNA Abundance. Cell Reports27, 3097–3106 (2019).Yco-corresponding authors
  • Haberman, N*, Huppertz, I*, Attig, J., König, J., Wang, Z., Hauer, C., Hentze, M.W., Kulozik, A.E., Le Hir, H., Curk, T., Sibley, C.R., Zarnack, K., Ule, J. Insights into the design and interpretation of iCLIP experiments. Genome Biology18, 7 (2017). *co-first authors
  • Chan, S.L., Huppertz, I., Yao, C., Weng, L., Moresco, J.J., Yates, J.R., Ule, J., Manley, J.L., Shi, Y. CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3’ processing. Genes Dev28, 2370–2380 (2014).
  • Huppertz, I., Attig, J., D’Ambrogio, A., Easton, L.E., Sibley, C.R., Sugimoto, Y., Tajnik, M., König, J., Ule, J. iCLIP: protein–RNA interactions at nucleotide resolution. Methods65, 274–287 (2014).